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PubMed2004

An adaptive and iterative algorithm for refining multiple sequence alignment.

Multiple sequence alignment is a basic tool in computational genomics. The art of multiple sequence alignment is about placing gaps. This paper presents a heuristic algorithm that improves multiple protein sequences alignment iteratively. A consistency-based objective function is used to evaluate the candidate moves. During the iterative optimization, well-aligned regions can be detected and kept intact. Columns of gaps will be inserted to assist the algorithm to escape from local optimal alignments. The algorithm has been evaluated using the BAliBASE benchmark alignment database. Results show that the performance of the algorithm does not depend on initial or seed alignments much. Given a perfect consistency library, the algorithm is able to produce alignments that are close to the global optimum. We demonstrate that the algorithm is able to refine alignments produced by other software, including ClustalW, SAGA and T-COFFEE. The program is available upon request.

Algorithms↗

PubMed2006

Cancer gene search with data-mining and genetic algorithms.

Cancer leads to approximately 25% of all mortalities, making it the second leading cause of death in the United States. Early and accurate detection of cancer is critical to the well being of patients. Analysis of gene expression data leads to cancer identification and classification, which will facilitate proper treatment selection and drug development. Gene expression data sets for ovarian, prostate, and lung cancer were analyzed in this research. An integrated gene-search algorithm for genetic expression data analysis was proposed. This integrated algorithm involves a genetic algorithm and correlation-based heuristics for data preprocessing (on partitioned data sets) and data mining (decision tree and support vector machines algorithms) for making predictions. Knowledge derived by the proposed algorithm has high classification accuracy with the ability to identify the most significant genes. Bagging and stacking algorithms were applied to further enhance the classification accuracy. The results were compared with that reported in the literature. Mapping of genotype information to the phenotype parameters will ultimately reduce the cost and complexity of cancer detection and classification.

Algorithms↗

PubMedDate not supplied

Optimisation of the predictive ability of artificial neural network (ANN) models: a comparison of three ANN programs and four classes of training algorithm.

The purpose of this study was to determine whether artificial neural network (ANN) programs implementing different backpropagation algorithms and default settings are capable of generating equivalent highly predictive models. Three ANN packages were used: INForm, CAD/Chem and MATLAB. Twenty variants of gradient descent, conjugate gradient, quasi-Newton and Bayesian regularization algorithms were used to train networks containing a single hidden layer of 3-12 nodes. All INForm and CAD/Chem models trained satisfactorily for tensile strength, disintegration time and percentage dissolution at 15, 30, 45 and 60 min. Similarly, acceptable training was obtained for MATLAB models using Bayesian regularization. Training of MATLAB models with other algorithms was erratic. This effect was attributed to a tendency for the MATLAB implementation of the algorithms to attenuate training in local minima of the error surface. Predictive models for tablet capping and friability could not be generated. The most predictive models from each ANN package varied with respect to the optimum network architecture and training algorithm. No significant differences were found in the predictive ability of these models. It is concluded that comparable models are obtainable from different ANN programs provided that both the network architecture and training algorithm are optimised. A broad strategy for optimisation of the predictive ability of an ANN model is proposed.

Algorithms↗

PubMed2004

Atrial pacing for prevention of atrial fibrillation: assessment of simultaneously implemented algorithms.

AIMS: Several preliminary studies indicated that right atrial pacing could prevent atrial tachyarrhythmias (ATA). We sought to compare the safety and the efficacy of atrial-based pacing supplemented by dedicated combined algorithms with conventional atrial pacing in the prevention of ATA. METHODS: Fifty-five patients with a history of recurrent paroxysmal ATA implanted with a dual-chamber pacemaker were studied during two randomized cross-over pacing periods (conventional DDD and DDD with ATA prevention algorithms) of 6 months duration. The primary endpoint was the burden of ATA episodes recorded by the device mode switch algorithm. RESULTS: The cross-over analysis did not demonstrate any significant difference between the two pacing modes: 254+/-533 h of ATA during the control period versus 238+/-518 h during the ATA prevention period. Analysis of a subgroup of patients found that those with the lower percentage of ventricular pacing benefited from ATA prevention algorithms (120+/-182 h versus 225+/-350 h during the control period; P < 0.04). CONCLUSION: When compared with DDD pacing at 70 bpm, ATA prevention algorithms have not demonstrated significant efficacy. However, a subgroup of patients with preserved native AV conduction (low percentage of ventricular pacing) responded to ATA prevention algorithms.

Aged↗

PubMed2006

Artificial neural network algorithms for early diagnosis of acute myocardial infarction and prediction of infarct size in chest pain patients.

BACKGROUND: To prospectively validate artificial neural network (ANN)-algorithms for early diagnosis of myocardial infarction (AMI) and prediction of 'major infarct' size in patients with chest pain and without ECG changes diagnostic for AMI. METHODS: Results of early and frequent Stratus CS measurements of troponin I (TnI) and myoglobin in 310 patients were used to validate four prespecified ANN-algorithms with use of cross-validation techniques. Two separate biochemical criteria for diagnosis of AMI were applied: TnI > or = 0.1 microg/L within 24 h ('TnI 0.1 AMI') and TnI > or = 0.4 microg/L within 24 h ('TnI 0.4 AMI'). To be considered clinically useful, the ANN-indications of AMI had to achieve a predefined positive predictive value (PPV) > or = 78% and a negative predictive value (NPV) > or = 94% at 2 h after admission. 'Major infarct' size was defined by peak levels of CK-MB within 24 h. RESULTS: For the best performing ANN-algorithms, the PPV and NPV for the indication of 'TnI 0.1 AMI' were 87% (p=0.009) and 99% (p=0.0001) at 2 h, respectively. For the indication of 'TnI 0.4 AMI', the PPV and NPV were 90% (p=0.006) and 99% (p=0.0004), respectively. Another ANN-algorithm predicted 'major AMI' at 2 h with a sensitivity of 96% and a specificity of 78%. Corresponding PPV and NPV were 73% and 97%, respectively. CONCLUSIONS: Specially designed ANN-algorithms allow diagnosis of AMI within 2 h of monitoring. These algorithms also allow early prediction of 'major AMI' size and could thus, be used as a valuable instrument for rapid assessment of chest pain patients.

Algorithms↗

PubMed2007

The CASH (color, architecture, symmetry, and homogeneity) algorithm for dermoscopy.

BACKGROUND: The color, architecture, symmetry, and homogeneity (CASH) algorithm for dermoscopy includes a feature not used in prior algorithms, namely, architecture. Architectural order/disorder is derived from current concepts regarding the biology of benign versus malignant melanocytic neoplasms. OBJECTIVE: We sought to evaluate the accuracy of the CASH algorithm. METHODS: A total CASH score (TCS) was calculated for dermoscopic images of 325 melanocytic neoplasms. Sensitivity, specificity, diagnostic accuracy, and receiver operating characteristic curve analyses were performed by comparing the TCS with the histopathologic diagnoses for all lesions. RESULTS: The mean TCS was 12.28 for melanoma, 7.62 for dysplastic nevi, and 5.24 for nondysplastic nevi. These differences were statistically significant (P < .001). A TCS of 8 or more yielded a sensitivity of 98% and specificity of 68% for the diagnosis of melanoma. LIMITATIONS: This is a single-evaluator pilot study. Additional studies are needed to verify the CASH algorithm. CONCLUSIONS: The CASH algorithm can distinguish melanoma from melanocytic nevi with sensitivity and specificity comparable with other algorithms. Further study is warranted to determine its intraobserver and interobserver correlations.

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PubMed2006

A contact algorithm for density-based load estimation.

An algorithm, which includes contact interactions within a joint, has been developed to estimate the dominant loading patterns in joints based on the density distribution of bone. The algorithm is applied to the proximal femur of a chimpanzee, gorilla and grizzly bear and is compared to the results obtained in a companion paper that uses a non-contact (linear) version of the density-based load estimation method. Results from the contact algorithm are consistent with those from the linear method. While the contact algorithm is substantially more complex than the linear method, it has some added benefits. First, since contact between the two interacting surfaces is incorporated into the load estimation method, the pressure distributions selected by the method are more likely indicative of those found in vivo. Thus, the pressure distributions predicted by the algorithm are more consistent with the in vivo loads that were responsible for producing the given distribution of bone density. Additionally, the relative positions of the interacting bones are known for each pressure distribution selected by the algorithm. This should allow the pressure distributions to be related to specific types of activities. The ultimate goal is to develop a technique that can predict dominant joint loading patterns and relate these loading patterns to specific types of locomotion and/or activities.

Algorithms↗

PubMed2003

The use of calculated epicardial potentials improves significantly the sensitivity of a diagnostic algorithm in the detection of acute myocardial infarction.

Inverse electrocardiography can calculate epicardial potentials (EP) from body surface potentials (BSP) taking into account a thoracic volume conductor model (TVCM). Previous studies have shown that a tailored TVCM is superior to a general TVCM in calculating EP. However, construction of a tailored TVCM for a patient in an acute clinical setting is impractical. In this study we used a general TVCM in our EP calculations to determine whether this improves detection of acute myocardial infarction (AMI) using a diagnostic algorithm. BSP were derived from the 80-lead body surface map (BSM). Consecutive patients (n=379) with ischemic type chest pain were recruited. The BSM and a 12-lead electrocardiogram (ECG) were recorded at initial presentation and creatine kinase (CK) and/or CK-MB were measured initially, 12 and 24 hours postsymptom onset. A physician interpreted the 12-lead electrocardiogram and documented ST elevation if present. AMI was defined by the World Health Organization (WHO) criteria. The diagnostic algorithm result for each patient using BSP and calculated EP were documented. AMI occurred in 171 patients. The diagnostic algorithm using BSP identified 106 of these as ST elevation AMI (STEMI) (sensitivity 62%, specificity 80%). The same algorithm using EP identified 133 as STEMI (sensitivity 78%, specificity 80%). Calculated EP improved the algorithm's diagnostic sensitivity by a factor of 1.25 (P<.001) with no significant difference in specificity. Calculated EP using a general TVCM significantly improves the sensitivity of a diagnostic algorithm based on BSP in detection of AMI with no significant loss in specificity.

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PubMed2005

Adaptive algorithms for first principal eigenvector computation.

The paper presents a unified framework to derive and analyze 10 different adaptive algorithms, some well-known, to compute the first principal eigenvector of the correlation matrix of a random vector sequence. Since adaptive principal eigenvector algorithms have originated from a diverse set of disciplines, including ad hoc methods, it is necessary to examine them in a unified framework. In a common framework consisting of five steps, we analyze the derivation, convergence, and rate results for many well-known algorithms as well as two new adaptive algorithms. In the process, we offer fresh perspectives on the known algorithms, and derive new results for others. The common framework also allows us to comparatively study the 10 algorithms. Finally, we show experimental results to support our analyses.

Algorithms↗

PubMed2006

Comparison among tomographic radionuclide ventriculography algorithms for computing left and right ventricular normal limits.

BACKGROUND: Various algorithms have been developed to compute right ventricular (RV) and left ventricular (LV) end-diastolic volumes, end-systolic volumes, and ejection fractions (EF) from tomographic radionuclide ventriculography (TRV). The aims of this investigation were to establish sex-specific normal limits, to determine whether different algorithms produce the same normal values, and to compare TRV normal limits vs for magnetic resonance imaging values in the literature. METHODS: Fifty-one healthy volunteers (29 men, 22 women) were studied prospectively. All subjects had normal electrocardiograms and echocardiographic examinations, and underwent both planar radionuclide ventriculography and TRV. Four algorithms were used to process TRV data. RESULTS: Normal limits for most functional parameters differed significantly from one algorithm to another. Volumes were greater in men, but no statistically significant differences were found between men and women for LV EF or RV EF values for any method. Normal LV and RV EF and volumes were largely consistent with the literature for cardiac magnetic resonance imaging. CONCLUSIONS: Ventricular measurements differ significantly among TRV algorithms. Therefore, it is important to apply sex-specific normal limits that are specific to a given TRV algorithm in interpreting LV and RV EF and volume measurements for each patient.

Adult↗

PubMed2004

Dosimetric verification of a commercial collapsed cone algorithm in simulated clinical situations.

BACKGROUND AND PURPOSE: This work reports a detailed study carried out in two UK radiotherapy centres of the dosimetric accuracy of the collapsed cone algorithm of a commercial treatment planning system (Helax-TMS) in simulated clinical situations. MATERIALS AND METHODS: Initially the accuracy of the collapsed cone algorithm in homogeneous media is evaluated for an extensive set of simple and complex fields. Water, lung and bone substitute epoxy resin material were then used to assess the algorithm in inhomogeneous media and compare its accuracy with the pencil beam algorithm currently in clinical use. Finally a semi-anatomic phantom and an anthropomorphic phantom were employed to assess the dosimetric accuracy using simulated clinical set ups. Thermoluminescence dosimeter (TLD) measurements were made with the anthropomorphic phantom and ionisation chambers otherwise. Nominal 4, 6 and 15 MV photon beams were studied. RESULTS: For most homogeneous cases agreement between measured and calculated dose is within +/-2% or +/-2 mm. In cases with heterogeneities and simulated clinical situations it is observed that the accuracy is also generally within +/-2% or +/-2 mm. Specific instances where the difference between measured and calculated values exceed this are highlighted. CONCLUSIONS: It can be concluded that in clinical treatment planning situations where lung is present the collapsed cone algorithm should be considered in preference to pencil beam algorithms normally used but that there may still be some discrepancy between calculations and measurement.

Algorithms↗

PubMed2005

Management of septic shock with a norepinephrine-based haemodynamic algorithm.

UNLABELLED: Management of septic shock (SS) with a norepinephrine (noradrenaline)-based haemodynamic algorithm. INTRODUCTION: The choice of the best vasopressor for haemodynamic management of septic shock is controversial. Nevertheless, very few studies have been focused on evaluating different management algorithms. The aim of this study was to evaluate the performance of a norepinephrine (NE)-based management protocol. Experience with NE as the initial vasopressor, even if not comparative, could bring relevant data for planning future trails. We also wanted to evaluate the compliance of critical care physicians and nurses with haemodynamic management protocol. PATIENTS AND METHOD: A norepinephrine-based algorithm for the management of septic shock that commands different sequential interventions according to its requirements, was applied prospectively to 100 consecutive septic shock patients. RESULTS: Norepinephrine was used as the first vasoactive drug in all patients with a maximum dose of 0.31+/-0.3 microg kg(-1)min(-1) and an ICU mortality of 33%. Physicians applied correctly all the steps of the algorithm in 92% of the patients. Applying the algorithm, avoided the use of pulmonary artery catheter in 31 patients and led to use of lower doses of vasoactive agents than in many other clinical experiences. CONCLUSION: In conclusion, our data support extended use of an algorithm based on norepinephrine for treating septic shock patients. This is the first clinical study that uses NE as the initial vasopressor drug systematically, and although not comparative, the mortality rates adjusted to APACHE II, are comparable to other studies. It also gives support for future clinical trials comparing norepinephrine with dopamine in this setting.

Aged↗

PubMed2005

Preoperative evaluation of pancreatic cystic lesions: cost-benefit analysis and proposed management algorithm.

BACKGROUND: This study was performed to develop a management algorithm that accurately predicts the necessity of operative intervention and results in significant cost savings for patients with cystic pancreatic tumors. METHODS: We reviewed 60 patients treated between 1992 and 2003. Accuracy rates of tests used to differentiate benign from premalignant and malignant cysts were calculated. A management algorithm was generated that incorporated clinical presentation, radiologic findings, and selective use of endoscopic procedures. This algorithm was tested for predictive accuracy, and savings between actual management and proposed management were compared. RESULTS: There was an average of 3 preoperative tests performed per patient. Endoscopic procedures included endoscopic retrograde cholangiopancreatography in 21 patients and endoscopic ultrasound in 25 patients. A cyst fluid carcinoembryonic antigen (CEA) level of 158 ng/mL or greater had an accuracy rate of 87.5% that was significantly higher than endoscopic retrograde cholangiopancreatography (72%), endoscopic ultrasound morphology (45%), or endoscopic ultrasound cytology (66.7%). There was no combination of tests that provided greater accuracy than cyst fluid CEA level alone (P < .05). The management algorithm had a positive predictive value of 81%. The average actual cost of radiographic and endoscopic procedures was dollar 8,080 per patient. The proposed cost based on the algorithm was dollar 6,677 with a savings of dollar 1,403 per patient (P = .009). CONCLUSIONS: In patients with clinical symptoms or radiographic findings of mucinous or malignant tumors, further testing is excessive. Of endoscopic tests available, the cystic fluid CEA level most accurately predicts the presence of a mucinous neoplasm. A management algorithm based on presenting symptoms, radiographic findings, and cyst fluid CEA level provides a guideline for the evaluation of cystic lesions in the most cost-efficient manner while ensuring proper care.

Adult↗

PubMed1990

Comparative accuracy of the vectorcardiogram and electrocardiogram in the localization of the accessory pathway in patients with Wolff-Parkinson-White syndrome: validation of a new vectorcardiographic algorithm by intraoperative epicardial mapping and electrophysiologic studies.

The scalar electrocardiograms (ECGs) and vectorcardiograms (VCGs) of 41 patients with Wolff-Parkinson-White (WPW) syndrome were used to compare the accuracy of these techniques in the identification of the site of preexcitation. The location of the accessory pathway (AP) was determined by endocavitary electrophysiologic studies in all patients and the location was confirmed during intraoperative epicardial mapping in 28 of them. The ECGs were classified according to Gallagher's criteria and with Milstein's algorithm, whereas the VCGs were classified according to a new two-step algorithm. The presence of multiple accessory pathways and coexisting myocardial infarctions were major limitations in both the VCG and ECG classification procedures. In patients with a single accessory pathway, three AP localizations (right free ventricular wall, posterior, or left free ventricular wall) were identified with the first step of the VCG algorithm, with an overall sensitivity (96.5%), specificity (90.7%), and positive predictive values (80%) that were greater than those obtained with the ECG Milstein algorithm (77.1%, 91.5%, and 75%, respectively). The second step of the VCG algorithm made it possible to identify an AP location in one of the following sites: anterior right, lateral right, posterior right, posterior left, lateral left, or anterior left ventricle. The overall sensitivity, specificity, and positive predictive values were greater for the second step of the VCG algorithm than for the ECG criteria proposed by Gallagher (43.6% versus 39.3%, 92.1% versus 87.4%, and 51.5% versus 33.3%, respectively). It was concluded that the VCG seems to be more specific and sensitive than the ECG in the identification of the preexcitation site and should be given preference in the initial evaluation of the WPW syndrome.

Adult↗

PubMed1998

New Down syndrome screening algorithm: ultrasonographic biometry and multiple serum markers combined with maternal age.

OBJECTIVE: We compared the Down syndrome screening efficiency of a new algorithm that combines humerus length measurement and serum analytes versus that of the traditional triple-analyte serum screen. STUDY DESIGN: Humerus length measurements were obtained prospectively in 1743 midtrimester (14 to 24 weeks) singleton fetuses before genetic amniocentesis. All patients had triple-marker serum screening before amniocentesis. Data on humerus length were expressed as multiples of the median, and were normalized by log transformation. Backward multiple stepwise logistic regression analysis was performed to determine which combination of biometry and serum markers best predicted fetal Down syndrome. The screening efficiency of the traditional triple-analyte algorithm was compared with that of a new multivariate gaussian algorithm that combined biometry and serum markers. RESULTS: There were 31 (1.8%) fetuses with Down syndrome in the study population. In the regression analysis humerus length, human chorionic gonadotropin, alpha-fetoprotein, and maternal age were significant predictors of Down syndrome, but unconjugated estriol was not. The combined algorithm (humerus length, human chorionic gonadotropin, and alpha-fetoprotein and age) was superior to the traditional triple screen for Down syndrome detection. The sensitivities at fixed false-positive rates were consistently higher in the combination than in the triple-screen protocol. For example, at a 10% false-positive rate the sensitivities were 65.0% and 52.3%, respectively. Similarly, at a 15% false-positive rate the sensitivities were 73.5% and 55.0%, respectively. CONCLUSION: A new screening algorithm combining humerus length and serum analytes was superior to the traditional triple screen. Although we used a high-risk population in this study, it is expected that the observed superiority of the combination screen would persist in a population of younger women. The development of a combined biometric and serum analyte screening algorithm for estimating individual odds could represent an advance in prenatal Down syndrome screening.

Algorithms↗

PubMed1995

Assessment of radial aspheres by the Arc-step algorithm as implemented by the Keratron keratoscope.

PURPOSE: To assess the accuracy with which the Keratron (Optikon 2000, Rome, Italy) measured rotationally symmetric, radially aspheric test surfaces according to an arc-step profile reconstruction algorithm and to discriminate between error caused by the algorithm and error from other sources. METHODS: Height, local power, and axial power calculated from radius of curvature centered on the instrument's axis were reported by the Keratron for four surfaces that had radial profiles similar to normal corneas. The Keratron profile reconstruction algorithm was simulated by using ray tracing. Keratron measurements were compared with the surfaces' formulas and the ray-traced simulations. RESULTS: The heights reported by the Keratron were within 0.25 microns from the four surfaces at less than 3 mm from the keratoscope axis and generally within 1 micron of the height calculated from the surfaces' formulas. The Keratron's axial powers were within +/- 0.1 diopter of the simulation of the axial solution between 1 and 4 mm of the axis but were greater central to 1 mm and peripheral to 4 mm. The Keratron's local powers were within -0.25 diopters at less than 4 mm from the axis and peripherally were between +1.75 diopters and -0.75 diopter of power calculated from the surface's instantaneous radii of curvature. Height error because of the arc-step algorithm was less than -0.2 micron. CONCLUSIONS: The Keratron's arc-step profile reconstruction algorithm contributed to its ability to measure height more accurately than keratoscopes that use spherically biased algorithms and provided measurement of local power.

Algorithms↗

PubMed2000

Classifying incomplete spinal cord injury syndromes: algorithms based on the International Standards for Neurological and Functional Classification of Spinal Cord Injury Patients.

OBJECTIVE: To develop an objective and uniform means for classifying patients with incomplete spinal cord injury (SCI) according to SCI syndromes. DESIGN: Criteria for assigning the syndromes (defined by the International Standards for Neurological and Functional Classification of SCI Patients) were operationalized by means of sensory and motor scores and were incorporated into a set of six independent algorithms and two composite algorithms. SETTING: A regional SCI rehabilitation center in Canada. PATIENTS: SCI patients (n = 56) with incomplete injuries (American Spinal Injury Association classes B, C, D) and stable neurologic deficits. RESULTS: Individual algorithms allowed the highest classification rate but with some patients meeting the criteria for more than one syndrome. A composite, differential allocation algorithm, with selected thresholds at decision nodes, yielded a classification rate approximating that of the individual algorithms but without double classifications. CONCLUSIONS: The composite algorithm provided an objective and standardized means of assigning patients to syndromes based on clinically measurable sensory and motor scores. The thresholds used to implement criteria and the order of decision nodes greatly influenced the outcomes and may be adjusted to suit the needs of the classification, that is, embracing liberal or stringent criteria. Controversy remains about the interpretation of some syndromes, and many patients remain unclassifiable because of mixed clinical presentation.

Adult↗

PubMed1999

Reflex testing II: evaluation of an algorithm for use of cardiac markers in the assessment of emergency department patients with chest pain.

A reflex algorithm was developed and evaluated for the use of serum cardiac markers for the diagnosis and rule out of acute myocardial infarction (AMI), and risk stratification of unstable angina patients for those who present to emergency departments (ED) with chest pain. The process begins with testing of total CK and myoglobin at admission. Based on these results, the algorithm determines the need for subsequent testing for the CK-MB isoenzyme and cardiac troponin I (cTnI). The algorithm also directs the need for further blood collection and cardiac marker testing at 4, 8, and 12 h after presentation. A total of eleven stopping points were identified. For some of these stopping points, the algorithm concluded that further blood collections and testing was unnecessary and redundant. The algorithm was retrospectively evaluated on 101 non-consecutive chest pain patients who presented to the EDs at three hospitals. For the AMI group (n=34), six of nine possible different stopping points were reached: 64.7% of cases were diagnosed with the first sample at admission, an additional 32.3% after 4 h, and 2.9% at 8 h. The 12-h sample was not necessary for any of the AMI patients. For the non-AMI group (n=67), most reached the stopping point of no cardiac injury or risk. There were five unstable angina patients who had minor myocardial damage on the basis of a marginally increased cTnI. Of these, one patient subsequently suffered AMI, and three others required angioplasty or bypass surgery. Compared to performing four tests on all patient samples, the reflex algorithm would have reduced the number of necessary tests from 442 to 130 (71% reduction) for AMI patients, and 871 to 469 (46% reduction) for non-AMI patients, if prospectively implemented.

Algorithms↗